Interpretive Summary: Contaminated water causes about 60 billion cases of gastro-intestinal illness annually worldwide. The majority of these cases occur in rural areas of both developed and developing countries where water supply is polluted with a variety of pathogenic bacteria, viruses and parasites. In this study, the concentrations of different bacterial species such as heterotrophic bacteria, Escherichia coli, and Enterococcus were determined after running tertiary water from Santa Ana River through two separation columns and through the aquifer material for 15 d. The Enterococcus group is a subgroup of fecal streptococci that includes at least five species. They are differentiated from other streptococci by their ability to grow in higher pH (9.6) and temperature (45 deg C) and they are major contributors to poor water quality world-wide. Confirmation of Escherichia coli and enterococci by polymerase chain reaction (PCR) was more accurate than confirmation by biochemical test. The number of total bacterial composition was higher with the DNA-based method than in the RNA-based finger-prints. RNA-based fingerprints represent the community structure of active members, whereas DNA-based fingerprints aim at numerically abundant members. Therefore, active members of the community are a sub-population of that community that performs certain biological functions.

Technical Abstract:
Public health concerns about pathogens present in animal manure are emerging constraints to water supplies in many areas of the world. The aim of this study was to examine microbial community composition in aquifer material in an effort to understanding key processes that control the growth and mobility of pathogens through aquifer sediment. The concentrations of different bacterial species such as heterotrophic bacteria, Escherichia coli, and Enterococcus were determined after running tertiary water from Santa Ana River through two tanks containing aquifer material for 15 d. Total microbial community profiles were also compared by using eubacterial primers to amplify 16S rRNA genes from total bacterial DNA and RNA. PCR and reverse transcriptase (RT) PCR were used to amplify 16S ribosomal RNA, and the products were subjected to denaturing gradient gel electrophoresis (DGGE).Enterococcus faecalis primers targeted the ddl gene which encodes the D-Ala : D-Ala ligase and produces a 941 DNA base pair product upon amplification and primers for E. faecium which produce a 658 DNA base pair product were used to identify the two species in the samples. The PCR assay with the ddl gene was 100% accurate. The biochemical test overestimated the percentage of E. faecium in our samples. A more detailed analysis with 16S rRNA-DGGE showed a wide variety of cells from source water attached to the aquifer materials and resulted in metabolically active microbial species as determined by higher DGGE bands in the aquifer material in the filtration tanks due to biofilm formation. At the end of the experimental period, the aquifer material entered a stable population state, which was characterized by a greater diversity of DNA-based fingerprints compared to viable bacteria as determined by RT-PCR-DGGE. RNA-based fingerprints represent the community structure of active members, whereas DNA-based fingerprints represent numerically abundant members. Therefore, active members of the community are a sub-population of that community that performs certain biological functions.